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Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 3.1M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.95 58.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.437 α = 90 b = 166.437 β = 90 c = 171.932 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 2016-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 119.58 99.9 0.092 31.4 7.2 40427
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 100 0.425 0.921 4.83 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XQ3 3.2 119.58 38180 2100 99.42 0.19469 0.19085 0.1947 0.26432 0.2602 RANDOM 86.804
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.706 r_dihedral_angle_3_deg 17.374 r_dihedral_angle_4_deg 15.343 r_long_range_B_refined 10.685 r_long_range_B_other 10.684 r_mcangle_it 8.173 r_mcangle_other 8.172 r_scangle_other 7.786 r_dihedral_angle_1_deg 7.645 r_mcbond_it 5.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.706 r_dihedral_angle_3_deg 17.374 r_dihedral_angle_4_deg 15.343 r_long_range_B_refined 10.685 r_long_range_B_other 10.684 r_mcangle_it 8.173 r_mcangle_other 8.172 r_scangle_other 7.786 r_dihedral_angle_1_deg 7.645 r_mcbond_it 5.391 r_mcbond_other 5.391 r_scbond_it 5.16 r_scbond_other 5.16 r_angle_refined_deg 1.616 r_angle_other_deg 1.058 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13887 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing